From b7c5a56c4c2f81bf54e9feb527dc6c1435028843 Mon Sep 17 00:00:00 2001
From: Peter van 't Hof <p.j.van_t_hof@lumc.nl>
Date: Fri, 13 Feb 2015 14:43:36 +0100
Subject: [PATCH] Add job check to unit tests
---
.../sasc/biopet/pipelines/carp/CarpTest.scala | 38 ++++++++++++-------
1 file changed, 24 insertions(+), 14 deletions(-)
diff --git a/public/carp/src/test/scala/nl/lumc/sasc/biopet/pipelines/carp/CarpTest.scala b/public/carp/src/test/scala/nl/lumc/sasc/biopet/pipelines/carp/CarpTest.scala
index 7a4cf5bc7..f604b000f 100644
--- a/public/carp/src/test/scala/nl/lumc/sasc/biopet/pipelines/carp/CarpTest.scala
+++ b/public/carp/src/test/scala/nl/lumc/sasc/biopet/pipelines/carp/CarpTest.scala
@@ -2,17 +2,20 @@ package nl.lumc.sasc.biopet.pipelines.carp
import java.io.File
-import nl.lumc.sasc.biopet.core.config.{ConfigValueIndex, Config}
+import nl.lumc.sasc.biopet.core.config.Config
+import nl.lumc.sasc.biopet.extensions.bwa.BwaMem
+import nl.lumc.sasc.biopet.extensions.macs2.Macs2CallPeak
+import nl.lumc.sasc.biopet.extensions.picard.{ MergeSamFiles, SortSam }
import nl.lumc.sasc.biopet.utils.ConfigUtils
import org.broadinstitute.gatk.queue.QSettings
-import org.testng.annotations.{DataProvider, Test}
-import org.testng.annotations.{Test, DataProvider}
-import org.scalatest.Assertions._
+import org.testng.annotations.{ Test, DataProvider }
+import org.scalatest.Matchers
+import org.scalatest.testng.TestNGSuite
/**
* Created by pjvan_thof on 2/13/15.
*/
-class CarpTest {
+class CarpTest extends TestNGSuite with Matchers {
def initPipeline(map: Map[String, Any]): Carp = {
new Carp() {
override def configName = "carp"
@@ -26,12 +29,11 @@ class CarpTest {
def carpOptions = {
val bool = Array(true, false)
- for (s1 <- bool; s2 <- bool; s3 <- bool; t <- bool; c <- bool) yield
- Array("", s1, s2, s3, t, c)
+ for (s1 <- bool; s2 <- bool; s3 <- bool; t <- bool; c <- bool) yield Array("", s1, s2, s3, t, c)
}
@Test(dataProvider = "carpOptions")
- def testCarp(f:String, sample1:Boolean, sample2:Boolean, sample3:Boolean, threatment:Boolean, control:Boolean): Unit = {
+ def testCarp(f: String, sample1: Boolean, sample2: Boolean, sample3: Boolean, threatment: Boolean, control: Boolean): Unit = {
val map = {
var m = ConfigUtils.mergeMaps(Map("output_dir" -> CarpTest.outputDir
), CarpTest.excutables)
@@ -55,8 +57,16 @@ class CarpTest {
} else { // When samples are correct
val carp = initPipeline(map)
carp.script()
+ val numberLibs = (if (sample1) 1 else 0) + (if (sample2) 1 else 0) + (if (sample3) 2 else 0) +
+ (if (threatment) 1 else 0) + (if (control) 1 else 0)
+ val numberSamples = (if (sample1) 1 else 0) + (if (sample2) 1 else 0) + (if (sample3) 1 else 0) +
+ (if (threatment) 1 else 0) + (if (control) 1 else 0)
+ carp.functions.count(_.isInstanceOf[BwaMem]) shouldBe numberLibs
+ carp.functions.count(_.isInstanceOf[SortSam]) shouldBe numberLibs
+ carp.functions.count(_.isInstanceOf[MergeSamFiles]) shouldBe (if (sample3) 1 else 0)
+ carp.functions.count(_.isInstanceOf[Macs2CallPeak]) shouldBe (numberSamples + (if (threatment) 1 else 0))
}
}
}
@@ -76,7 +86,7 @@ object CarpTest {
)
val sample1 = Map(
- "samples" -> Map( "sample1" -> Map( "libraries" -> Map(
+ "samples" -> Map("sample1" -> Map("libraries" -> Map(
"lib1" -> Map(
"R1" -> "1_1_R1.fq",
"R2" -> "1_1_R2.fq"
@@ -85,16 +95,16 @@ object CarpTest {
)))
val sample2 = Map(
- "samples" -> Map( "sample2" -> Map( "libraries" -> Map(
+ "samples" -> Map("sample2" -> Map("libraries" -> Map(
"lib1" -> Map(
"R1" -> "2_1_R1.fq",
"R2" -> "2_1_R2.fq"
)
)
- )))
+ )))
val sample3 = Map(
- "samples" -> Map( "sample3" -> Map( "libraries" -> Map(
+ "samples" -> Map("sample3" -> Map("libraries" -> Map(
"lib1" -> Map(
"R1" -> "3_1_R1.fq",
"R2" -> "3_1_R2.fq"
@@ -107,7 +117,7 @@ object CarpTest {
)))
val threatment1 = Map(
- "samples" -> Map( "threatment" -> Map( "control" -> "control1","libraries" -> Map(
+ "samples" -> Map("threatment" -> Map("control" -> "control1", "libraries" -> Map(
"lib1" -> Map(
"R1" -> "threatment_1_R1.fq",
"R2" -> "threatment_1_R2.fq"
@@ -116,7 +126,7 @@ object CarpTest {
)))
val control1 = Map(
- "samples" -> Map( "control1" -> Map( "libraries" -> Map(
+ "samples" -> Map("control1" -> Map("libraries" -> Map(
"lib1" -> Map(
"R1" -> "control_1_R1.fq",
"R2" -> "control_1_R2.fq"
--
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